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Yorodumi- PDB-4wu2: Structure of the PTP-like myo-inositol phosphatase from Selenomon... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4wu2 | |||||||||
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Title | Structure of the PTP-like myo-inositol phosphatase from Selenomonas ruminantium in complex with myo-inositol-(1,4,5)-trikisphosphate | |||||||||
Components | Myo-inositol phosphohydrolase | |||||||||
Keywords | HYDROLASE | |||||||||
Function / homology | Function and homology information | |||||||||
Biological species | Selenomonas ruminantium (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å | |||||||||
Authors | Bruder, L.M. / Mosimann, S.C. | |||||||||
Funding support | Canada, 2items
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Citation | Journal: To Be Published Title: Structure of the PTP-like phytase from Selenomonas ruminantium in complex with myo-inositol-(1,4,5)-trikisphosphate Authors: Bruder, L.M. #1: Journal: J. Biol. Chem. / Year: 2012 Title: Substrate binding in protein-tyrosine phosphatase-like inositol polyphosphatases. Authors: Gruninger, R.J. / Dobing, S. / Smith, A.D. / Bruder, L.M. / Selinger, L.B. / Wieden, H.J. / Mosimann, S.C. #2: Journal: FEBS J. / Year: 2008 Title: Effect of ionic strength and oxidation on the P-loop conformation of the protein tyrosine phosphatase-like phytase, PhyAsr. Authors: Gruninger, R.J. / Selinger, L.B. / Mosimann, S.C. #3: Journal: Protein Sci. / Year: 2007 Title: Kinetic and structural analysis of a bacterial protein tyrosine phosphatase-like myo-inositol polyphosphatase. Authors: Puhl, A.A. / Gruninger, R.J. / Greiner, R. / Janzen, T.W. / Mosimann, S.C. / Selinger, L.B. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4wu2.cif.gz | 155.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4wu2.ent.gz | 120.8 KB | Display | PDB format |
PDBx/mmJSON format | 4wu2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4wu2_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 4wu2_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 4wu2_validation.xml.gz | 28.6 KB | Display | |
Data in CIF | 4wu2_validation.cif.gz | 42.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wu/4wu2 ftp://data.pdbj.org/pub/pdb/validation_reports/wu/4wu2 | HTTPS FTP |
-Related structure data
Related structure data | 3mmjS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 39130.000 Da / Num. of mol.: 2 / Fragment: UNP residues 28-346 / Mutation: C252S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Selenomonas ruminantium (bacteria) / Gene: phyA / Plasmid: pET28b / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q7WUJ1, 3-phytase |
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-Non-polymers , 5 types, 493 molecules
#2: Chemical | #3: Chemical | #4: Chemical | ChemComp-GOL / #5: Chemical | ChemComp-CL / | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.16 Å3/Da / Density % sol: 61.08 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.8 Details: PEG 8000, sodium acetate, sodium chloride, beta-mercapto ethanol |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97934 Å | |||||||||||||||
Detector | Type: RAYONIX MX-300 / Detector: CCD / Date: Feb 4, 2011 | |||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||
Radiation wavelength | Wavelength: 0.97934 Å / Relative weight: 1 | |||||||||||||||
Reflection twin |
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Reflection | Resolution: 2→44.9 Å / Num. obs: 65377 / % possible obs: 99.9 % / Redundancy: 3.3 % / Rmerge(I) obs: 0.128 / Net I/σ(I): 5.2 | |||||||||||||||
Reflection shell | Resolution: 2.15→2.22 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.523 / Mean I/σ(I) obs: 1.9 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3MMJ Resolution: 2.15→44.89 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.925 / SU B: 5.931 / SU ML: 0.143 / Cross valid method: THROUGHOUT / ESU R: 0.195 / ESU R Free: 0.161 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 31.039 Å2
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Refinement step | Cycle: LAST / Resolution: 2.15→44.89 Å
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